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Sylvain Tricot 2025-07-18 17:22:25 +02:00
parent 78245306b1
commit 77adea5b1b
23 changed files with 296 additions and 271 deletions
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2
msspecbook/_build/html/.buildinfo
View File

@ -1,4 +1,4 @@
# Sphinx build info version 1
# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
config: 0b896abf2c995b3493312dcbe0e8b47f
config: d64285b76259d47aa1d35d9bc7e7829a
tags: 645f666f9bcd5a90fca523b33c5a78b7

2
msspecbook/_build/html/Activity01/Activity01.html
View File

@ -189,7 +189,7 @@
<li class="toctree-l1"><a class="reference internal" href="../Activity07/Activity07.html">Activity 7: Large clusters and path filtering</a></li>
<li class="toctree-l1"><a class="reference internal" href="../Activity08/Activity08.html">Activity 8: Inequivalent emitters and the XPD of a substrate</a></li>
<li class="toctree-l1"><a class="reference internal" href="../Activity09/Activity09.html">Activity 9: Comparing simulation and experiment with R-factors</a></li>
<li class="toctree-l1"><a class="reference internal" href="../Activity10/Activity10.html">Activity 10: Auger Electron Diffraction</a></li>
<li class="toctree-l1"><a class="reference internal" href="../Activity10/Activity10.html">Activity 10: Parallelization and multi-processing in MsSpec</a></li>
<li class="toctree-l1"><a class="reference internal" href="../Activity11/Activity11.html">Activity 11: Spectral radius and convergence</a></li>
<li class="toctree-l1"><a class="reference internal" href="../backmatter.html">Final word</a></li>
</ul>

178
msspecbook/_build/html/Activity02/Activity02.html
View File

@ -191,7 +191,7 @@
<li class="toctree-l1"><a class="reference internal" href="../Activity07/Activity07.html">Activity 7: Large clusters and path filtering</a></li>
<li class="toctree-l1"><a class="reference internal" href="../Activity08/Activity08.html">Activity 8: Inequivalent emitters and the XPD of a substrate</a></li>
<li class="toctree-l1"><a class="reference internal" href="../Activity09/Activity09.html">Activity 9: Comparing simulation and experiment with R-factors</a></li>
<li class="toctree-l1"><a class="reference internal" href="../Activity10/Activity10.html">Activity 10: Auger Electron Diffraction</a></li>
<li class="toctree-l1"><a class="reference internal" href="../Activity10/Activity10.html">Activity 10: Parallelization and multi-processing in MsSpec</a></li>
<li class="toctree-l1"><a class="reference internal" href="../Activity11/Activity11.html">Activity 11: Spectral radius and convergence</a></li>
<li class="toctree-l1"><a class="reference internal" href="../backmatter.html">Final word</a></li>
</ul>
@ -467,7 +467,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution
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@ -499,7 +499,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution
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@ -515,7 +515,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution
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@ -523,7 +523,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution
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@ -531,7 +531,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution
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@ -539,7 +539,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution
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@ -547,7 +547,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution
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@ -555,7 +555,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution
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@ -563,7 +563,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution
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@ -571,7 +571,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution
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@ -579,7 +579,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution
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@ -587,7 +587,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution
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@ -595,7 +595,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution
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@ -603,7 +603,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution
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@ -611,7 +611,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution
<sphere radius="1.45"/>
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@ -619,7 +619,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution
<sphere radius="1.45"/>
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@ -627,7 +627,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution
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@ -683,7 +683,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution
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@ -707,7 +707,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution
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@ -715,7 +715,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution
<sphere radius="1.45"/>
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@ -723,7 +723,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution
<sphere radius="1.45"/>
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@ -731,7 +731,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution
<sphere radius="1.45"/>
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@ -771,7 +771,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution
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@ -779,7 +779,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution
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@ -787,7 +787,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution
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@ -795,7 +795,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution
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@ -803,7 +803,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution
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@ -811,7 +811,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution
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@ -819,7 +819,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution
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@ -827,7 +827,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution
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@ -835,7 +835,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution
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@ -843,7 +843,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution
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@ -851,7 +851,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution
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@ -859,7 +859,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution
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@ -867,7 +867,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution
<sphere radius="1.45"/>
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@ -875,7 +875,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution
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@ -883,7 +883,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution
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@ -891,7 +891,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution
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@ -899,7 +899,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution
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@ -907,7 +907,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution
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@ -915,7 +915,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution
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@ -923,7 +923,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution
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@ -931,7 +931,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution
<sphere radius="1.45"/>
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@ -939,7 +939,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution
<sphere radius="1.45"/>
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</transform>
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@ -947,7 +947,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution
<sphere radius="1.45"/>
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</transform>
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@ -955,7 +955,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution
<sphere radius="1.45"/>
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@ -971,7 +971,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution
<sphere radius="1.45"/>
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@ -979,7 +979,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution
<sphere radius="1.45"/>
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@ -987,7 +987,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution
<sphere radius="1.45"/>
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<transform translation="-0.8348677539985943 1.4460333675264891 -2.3613439014783584">
<shape>
<appearance>
<material diffuseColor="0.753 0.753 0.753"/>
@ -1027,7 +1027,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution
<sphere radius="1.45"/>
</shape>
</transform>
<transform translation="1.6697355079972027 8.676200205158935 -2.361343901478344">
<transform translation="1.6697355079972027 8.676200205158942 -2.3613439014783584">
<shape>
<appearance>
<material diffuseColor="0.753 0.753 0.753"/>
@ -1035,7 +1035,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution
<sphere radius="1.45"/>
</shape>
</transform>
<transform translation="-0.8348677539986014 7.230166837632446 -2.3613439014783584">
<transform translation="-0.8348677539985943 7.230166837632453 -2.3613439014783584">
<shape>
<appearance>
<material diffuseColor="0.753 0.753 0.753"/>
@ -1043,7 +1043,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution
<sphere radius="1.45"/>
</shape>
</transform>
<transform translation="-2.504603261995797 7.230166837632446 1.869950721400393e-05">
<transform translation="-2.504603261995797 7.230166837632453 1.869950721400393e-05">
<shape>
<appearance>
<material diffuseColor="0.753 0.753 0.753"/>
@ -1051,7 +1051,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution
<sphere radius="1.45"/>
</shape>
</transform>
<transform translation="0.0 5.784133470105957 1.869950721400393e-05">
<transform translation="0.0 5.78413347010596 1.869950721400393e-05">
<shape>
<appearance>
<material diffuseColor="0.753 0.753 0.753"/>
@ -1059,7 +1059,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution
<sphere radius="1.45"/>
</shape>
</transform>
<transform translation="0.0 8.676200205158935 1.869950721400393e-05">
<transform translation="0.0 8.676200205158942 1.869950721400393e-05">
<shape>
<appearance>
<material diffuseColor="0.753 0.753 0.753"/>
@ -1075,7 +1075,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution
<sphere radius="1.45"/>
</shape>
</transform>
<transform translation="5.844074277990202 -1.4460333675264962 -4.7227065024639305">
<transform translation="5.844074277990202 -1.4460333675264891 -4.722706502463916">
<shape>
<appearance>
<material diffuseColor="0.753 0.753 0.753"/>
@ -1083,7 +1083,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution
<sphere radius="1.45"/>
</shape>
</transform>
<transform translation="8.348677539986 -7.105427357601002e-15 -4.7227065024639305">
<transform translation="8.348677539986 0.0 -4.722706502463916">
<shape>
<appearance>
<material diffuseColor="0.753 0.753 0.753"/>
@ -1091,7 +1091,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution
<sphere radius="1.45"/>
</shape>
</transform>
<transform translation="5.844074277990202 -4.3381001025794745 -4.7227065024639305">
<transform translation="5.844074277990202 -4.338100102579467 -4.7227065024639305">
<shape>
<appearance>
<material diffuseColor="0.753 0.753 0.753"/>
@ -1099,7 +1099,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution
<sphere radius="1.45"/>
</shape>
</transform>
<transform translation="4.174338769993 -4.3381001025794745 -2.3613439014783584">
<transform translation="4.174338769993 -4.338100102579467 -2.3613439014783584">
<shape>
<appearance>
<material diffuseColor="0.753 0.753 0.753"/>
@ -1107,7 +1107,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution
<sphere radius="1.45"/>
</shape>
</transform>
<transform translation="6.678942031988804 -5.784133470105964 -2.3613439014783584">
<transform translation="6.678942031988804 -5.784133470105957 -2.3613439014783584">
<shape>
<appearance>
<material diffuseColor="0.753 0.753 0.753"/>
@ -1115,7 +1115,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution
<sphere radius="1.45"/>
</shape>
</transform>
<transform translation="6.678942031988804 -2.8920667350529854 -2.3613439014783584">
<transform translation="6.678942031988804 -2.8920667350529783 -2.3613439014783584">
<shape>
<appearance>
<material diffuseColor="0.753 0.753 0.753"/>
@ -1123,7 +1123,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution
<sphere radius="1.45"/>
</shape>
</transform>
<transform translation="4.174338769993 -7.230166837632453 -2.3613439014783584">
<transform translation="4.174338769993 -7.230166837632446 -2.3613439014783584">
<shape>
<appearance>
<material diffuseColor="0.753 0.753 0.753"/>
@ -1131,7 +1131,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution
<sphere radius="1.45"/>
</shape>
</transform>
<transform translation="2.504603261995804 -7.230166837632453 1.869950721400393e-05">
<transform translation="2.504603261995804 -7.230166837632446 1.869950721400393e-05">
<shape>
<appearance>
<material diffuseColor="0.753 0.753 0.753"/>
@ -1139,7 +1139,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution
<sphere radius="1.45"/>
</shape>
</transform>
<transform translation="5.009206523991601 -5.784133470105964 1.869950721400393e-05">
<transform translation="5.009206523991601 -5.784133470105957 1.869950721400393e-05">
<shape>
<appearance>
<material diffuseColor="0.753 0.753 0.753"/>
@ -1147,7 +1147,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution
<sphere radius="1.45"/>
</shape>
</transform>
<transform translation="5.844074277990195 4.33810010257946 -4.722706502463916">
<transform translation="5.844074277990195 4.3381001025794745 -4.722706502463916">
<shape>
<appearance>
<material diffuseColor="0.753 0.753 0.753"/>
@ -1155,7 +1155,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution
<sphere radius="1.45"/>
</shape>
</transform>
<transform translation="5.844074277990202 1.446033367526482 -4.7227065024639305">
<transform translation="5.844074277990202 1.4460333675264962 -4.7227065024639305">
<shape>
<appearance>
<material diffuseColor="0.753 0.753 0.753"/>
@ -1163,7 +1163,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution
<sphere radius="1.45"/>
</shape>
</transform>
<transform translation="4.174338769993 1.446033367526482 -2.3613439014783584">
<transform translation="4.174338769993 1.4460333675264962 -2.3613439014783584">
<shape>
<appearance>
<material diffuseColor="0.753 0.753 0.753"/>
@ -1171,7 +1171,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution
<sphere radius="1.45"/>
</shape>
</transform>
<transform translation="6.678942031988797 -7.105427357601002e-15 -2.3613439014783584">
<transform translation="6.678942031988797 7.105427357601002e-15 -2.3613439014783584">
<shape>
<appearance>
<material diffuseColor="0.753 0.753 0.753"/>
@ -1179,7 +1179,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution
<sphere radius="1.45"/>
</shape>
</transform>
<transform translation="6.678942031988797 2.892066735052971 -2.3613439014783584">
<transform translation="6.678942031988797 2.8920667350529854 -2.3613439014783584">
<shape>
<appearance>
<material diffuseColor="0.753 0.753 0.753"/>
@ -1187,7 +1187,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution
<sphere radius="1.45"/>
</shape>
</transform>
<transform translation="4.174338769993 -1.4460333675264962 -2.3613439014783584">
<transform translation="4.174338769993 -1.4460333675264891 -2.3613439014783584">
<shape>
<appearance>
<material diffuseColor="0.753 0.753 0.753"/>
@ -1195,7 +1195,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution
<sphere radius="1.45"/>
</shape>
</transform>
<transform translation="2.504603261995797 -1.4460333675264962 1.869950721400393e-05">
<transform translation="2.504603261995797 -1.4460333675264891 1.869950721400393e-05">
<shape>
<appearance>
<material diffuseColor="0.753 0.753 0.753"/>
@ -1203,7 +1203,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution
<sphere radius="1.45"/>
</shape>
</transform>
<transform translation="5.009206523991601 -2.8920667350529854 1.869950721400393e-05">
<transform translation="5.009206523991601 -2.8920667350529783 1.869950721400393e-05">
<shape>
<appearance>
<material diffuseColor="0.753 0.753 0.753"/>
@ -1211,7 +1211,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution
<sphere radius="1.45"/>
</shape>
</transform>
<transform translation="5.009206523991601 -7.105427357601002e-15 1.869950721400393e-05">
<transform translation="5.009206523991601 0.0 1.869950721400393e-05">
<shape>
<appearance>
<material diffuseColor="0.753 0.753 0.753"/>
@ -1219,7 +1219,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution
<sphere radius="1.45"/>
</shape>
</transform>
<transform translation="2.504603261995797 -4.3381001025794745 1.869950721400393e-05">
<transform translation="2.504603261995797 -4.338100102579467 1.869950721400393e-05">
<shape>
<appearance>
<material diffuseColor="0.753 0.753 0.753"/>
@ -1227,7 +1227,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution
<sphere radius="1.45"/>
</shape>
</transform>
<transform translation="4.174338769993 7.230166837632446 -2.3613439014783584">
<transform translation="4.174338769993 7.230166837632453 -2.3613439014783584">
<shape>
<appearance>
<material diffuseColor="0.753 0.753 0.753"/>
@ -1235,7 +1235,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution
<sphere radius="1.45"/>
</shape>
</transform>
<transform translation="6.678942031988797 5.784133470105957 -2.3613439014783584">
<transform translation="6.678942031988797 5.784133470105964 -2.3613439014783584">
<shape>
<appearance>
<material diffuseColor="0.753 0.753 0.753"/>
@ -1243,7 +1243,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution
<sphere radius="1.45"/>
</shape>
</transform>
<transform translation="4.174338769993 4.338100102579467 -2.3613439014783584">
<transform translation="4.174338769993 4.3381001025794745 -2.3613439014783584">
<shape>
<appearance>
<material diffuseColor="0.753 0.753 0.753"/>
@ -1251,7 +1251,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution
<sphere radius="1.45"/>
</shape>
</transform>
<transform translation="2.504603261995797 4.338100102579467 1.869950721400393e-05">
<transform translation="2.504603261995797 4.3381001025794745 1.869950721400393e-05">
<shape>
<appearance>
<material diffuseColor="0.753 0.753 0.753"/>
@ -1259,7 +1259,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution
<sphere radius="1.45"/>
</shape>
</transform>
<transform translation="5.009206523991601 2.8920667350529783 1.869950721400393e-05">
<transform translation="5.009206523991601 2.8920667350529854 1.869950721400393e-05">
<shape>
<appearance>
<material diffuseColor="0.753 0.753 0.753"/>
@ -1267,7 +1267,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution
<sphere radius="1.45"/>
</shape>
</transform>
<transform translation="5.009206523991601 5.784133470105957 1.869950721400393e-05">
<transform translation="5.009206523991601 5.784133470105964 1.869950721400393e-05">
<shape>
<appearance>
<material diffuseColor="0.753 0.753 0.753"/>
@ -1283,7 +1283,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution
<sphere radius="1.45"/>
</shape>
</transform>
<transform translation="2.504603261995797 7.230166837632446 1.869950721400393e-05">
<transform translation="2.504603261995797 7.230166837632453 1.869950721400393e-05">
<shape>
<appearance>
<material diffuseColor="0.753 0.753 0.753"/>
@ -1291,7 +1291,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution
<sphere radius="1.45"/>
</shape>
</transform>
<transform translation="9.183545293984608 -1.4460333675264962 -2.3613439014783584">
<transform translation="9.183545293984608 -1.4460333675264891 -2.3613439014783584">
<shape>
<appearance>
<material diffuseColor="0.753 0.753 0.753"/>
@ -1299,7 +1299,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution
<sphere radius="1.45"/>
</shape>
</transform>
<transform translation="7.513809785987405 -4.3381001025794745 1.869950721400393e-05">
<transform translation="7.513809785987405 -4.338100102579467 1.869950721400393e-05">
<shape>
<appearance>
<material diffuseColor="0.753 0.753 0.753"/>
@ -1307,7 +1307,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution
<sphere radius="1.45"/>
</shape>
</transform>
<transform translation="9.183545293984604 1.446033367526482 -2.3613439014783584">
<transform translation="9.183545293984604 1.4460333675264962 -2.361343901478344">
<shape>
<appearance>
<material diffuseColor="0.753 0.753 0.753"/>
@ -1315,7 +1315,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution
<sphere radius="1.45"/>
</shape>
</transform>
<transform translation="7.513809785987405 1.446033367526482 1.869950721400393e-05">
<transform translation="7.513809785987405 1.4460333675264962 1.8699507228214785e-05">
<shape>
<appearance>
<material diffuseColor="0.753 0.753 0.753"/>
@ -1323,7 +1323,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution
<sphere radius="1.45"/>
</shape>
</transform>
<transform translation="7.513809785987405 -1.4460333675264962 1.869950721400393e-05">
<transform translation="7.513809785987405 -1.4460333675264891 1.869950721400393e-05">
<shape>
<appearance>
<material diffuseColor="0.753 0.753 0.753"/>
@ -1331,7 +1331,7 @@ The idea is to use low energy photoelectron diffraction to see the substitution
<sphere radius="1.45"/>
</shape>
</transform>
<transform translation="7.513809785987405 4.338100102579467 1.869950721400393e-05">
<transform translation="7.513809785987405 4.3381001025794745 1.869950721400393e-05">
<shape>
<appearance>
<material diffuseColor="0.753 0.753 0.753"/>

2
msspecbook/_build/html/Activity03/Activity03.html
View File

@ -191,7 +191,7 @@
<li class="toctree-l1"><a class="reference internal" href="../Activity07/Activity07.html">Activity 7: Large clusters and path filtering</a></li>
<li class="toctree-l1"><a class="reference internal" href="../Activity08/Activity08.html">Activity 8: Inequivalent emitters and the XPD of a substrate</a></li>
<li class="toctree-l1"><a class="reference internal" href="../Activity09/Activity09.html">Activity 9: Comparing simulation and experiment with R-factors</a></li>
<li class="toctree-l1"><a class="reference internal" href="../Activity10/Activity10.html">Activity 10: Auger Electron Diffraction</a></li>
<li class="toctree-l1"><a class="reference internal" href="../Activity10/Activity10.html">Activity 10: Parallelization and multi-processing in MsSpec</a></li>
<li class="toctree-l1"><a class="reference internal" href="../Activity11/Activity11.html">Activity 11: Spectral radius and convergence</a></li>
<li class="toctree-l1"><a class="reference internal" href="../backmatter.html">Final word</a></li>
</ul>

2
msspecbook/_build/html/Activity04/Activity04.html
View File

@ -189,7 +189,7 @@
<li class="toctree-l1"><a class="reference internal" href="../Activity07/Activity07.html">Activity 7: Large clusters and path filtering</a></li>
<li class="toctree-l1"><a class="reference internal" href="../Activity08/Activity08.html">Activity 8: Inequivalent emitters and the XPD of a substrate</a></li>
<li class="toctree-l1"><a class="reference internal" href="../Activity09/Activity09.html">Activity 9: Comparing simulation and experiment with R-factors</a></li>
<li class="toctree-l1"><a class="reference internal" href="../Activity10/Activity10.html">Activity 10: Auger Electron Diffraction</a></li>
<li class="toctree-l1"><a class="reference internal" href="../Activity10/Activity10.html">Activity 10: Parallelization and multi-processing in MsSpec</a></li>
<li class="toctree-l1"><a class="reference internal" href="../Activity11/Activity11.html">Activity 11: Spectral radius and convergence</a></li>
<li class="toctree-l1"><a class="reference internal" href="../backmatter.html">Final word</a></li>
</ul>

14
msspecbook/_build/html/Activity05/Activity05.html
View File

@ -191,7 +191,7 @@
<li class="toctree-l1"><a class="reference internal" href="../Activity07/Activity07.html">Activity 7: Large clusters and path filtering</a></li>
<li class="toctree-l1"><a class="reference internal" href="../Activity08/Activity08.html">Activity 8: Inequivalent emitters and the XPD of a substrate</a></li>
<li class="toctree-l1"><a class="reference internal" href="../Activity09/Activity09.html">Activity 9: Comparing simulation and experiment with R-factors</a></li>
<li class="toctree-l1"><a class="reference internal" href="../Activity10/Activity10.html">Activity 10: Auger Electron Diffraction</a></li>
<li class="toctree-l1"><a class="reference internal" href="../Activity10/Activity10.html">Activity 10: Parallelization and multi-processing in MsSpec</a></li>
<li class="toctree-l1"><a class="reference internal" href="../Activity11/Activity11.html">Activity 11: Spectral radius and convergence</a></li>
<li class="toctree-l1"><a class="reference internal" href="../backmatter.html">Final word</a></li>
</ul>
@ -516,7 +516,7 @@ document.write(`
<!--Inserting Generated X3D Scene-->
<scene>
<viewpoint position="0 0 28.28">
<viewpoint position="0 0 28.28000000000003">
<group/>
</viewpoint>
<transform translation="-0.8837500000000003 -2.220446049250313e-16 -3.002">
@ -884,7 +884,7 @@ document.write(`
<sphere radius="1.2"/>
</shape>
</transform>
<transform translation="-7.070000000000007 0.0 4.6629367034256575e-15">
<transform translation="-7.070000000000022 0.0 4.6629367034256575e-15">
<shape>
<appearance>
<material diffuseColor="0.749 0.761 0.78"/>
@ -892,7 +892,7 @@ document.write(`
<sphere radius="1.6"/>
</shape>
</transform>
<transform translation="-7.070000000000007 2.040933201585325 1.724999999999999">
<transform translation="-7.070000000000022 2.040933201585325 1.724999999999999">
<shape>
<appearance>
<material diffuseColor="1.0 0.631 0.0"/>
@ -948,7 +948,7 @@ document.write(`
<sphere radius="1.2"/>
</shape>
</transform>
<transform translation="-1.7675000000000125 3.0613998023779985 4.6629367034256575e-15">
<transform translation="-1.7674999999999983 3.0613998023779985 4.6629367034256575e-15">
<shape>
<appearance>
<material diffuseColor="0.749 0.761 0.78"/>
@ -956,7 +956,7 @@ document.write(`
<sphere radius="1.6"/>
</shape>
</transform>
<transform translation="-1.7675000000000125 5.102333003963331 1.724999999999999">
<transform translation="-1.7674999999999983 5.102333003963331 1.724999999999999">
<shape>
<appearance>
<material diffuseColor="1.0 0.631 0.0"/>
@ -1004,7 +1004,7 @@ document.write(`
<sphere radius="1.6"/>
</shape>
</transform>
<transform translation="-3.5349999999999966 6.12279960475599 4.6629367034256575e-15">
<transform translation="-3.535000000000011 6.12279960475599 4.6629367034256575e-15">
<shape>
<appearance>
<material diffuseColor="0.749 0.761 0.78"/>

2
msspecbook/_build/html/Activity06/Activity06.html
View File

@ -191,7 +191,7 @@
<li class="toctree-l1"><a class="reference internal" href="../Activity07/Activity07.html">Activity 7: Large clusters and path filtering</a></li>
<li class="toctree-l1"><a class="reference internal" href="../Activity08/Activity08.html">Activity 8: Inequivalent emitters and the XPD of a substrate</a></li>
<li class="toctree-l1"><a class="reference internal" href="../Activity09/Activity09.html">Activity 9: Comparing simulation and experiment with R-factors</a></li>
<li class="toctree-l1"><a class="reference internal" href="../Activity10/Activity10.html">Activity 10: Auger Electron Diffraction</a></li>
<li class="toctree-l1"><a class="reference internal" href="../Activity10/Activity10.html">Activity 10: Parallelization and multi-processing in MsSpec</a></li>
<li class="toctree-l1"><a class="reference internal" href="../Activity11/Activity11.html">Activity 11: Spectral radius and convergence</a></li>
<li class="toctree-l1"><a class="reference internal" href="../backmatter.html">Final word</a></li>
</ul>

2
msspecbook/_build/html/Activity07/Activity07.html
View File

@ -191,7 +191,7 @@
<li class="toctree-l1 current active"><a class="current reference internal" href="#">Activity 7: Large clusters and path filtering</a></li>
<li class="toctree-l1"><a class="reference internal" href="../Activity08/Activity08.html">Activity 8: Inequivalent emitters and the XPD of a substrate</a></li>
<li class="toctree-l1"><a class="reference internal" href="../Activity09/Activity09.html">Activity 9: Comparing simulation and experiment with R-factors</a></li>
<li class="toctree-l1"><a class="reference internal" href="../Activity10/Activity10.html">Activity 10: Auger Electron Diffraction</a></li>
<li class="toctree-l1"><a class="reference internal" href="../Activity10/Activity10.html">Activity 10: Parallelization and multi-processing in MsSpec</a></li>
<li class="toctree-l1"><a class="reference internal" href="../Activity11/Activity11.html">Activity 11: Spectral radius and convergence</a></li>
<li class="toctree-l1"><a class="reference internal" href="../backmatter.html">Final word</a></li>
</ul>

263
msspecbook/_build/html/Activity08/Activity08.html
View File

@ -191,7 +191,7 @@
<li class="toctree-l1"><a class="reference internal" href="../Activity07/Activity07.html">Activity 7: Large clusters and path filtering</a></li>
<li class="toctree-l1 current active"><a class="current reference internal" href="#">Activity 8: Inequivalent emitters and the XPD of a substrate</a></li>
<li class="toctree-l1"><a class="reference internal" href="../Activity09/Activity09.html">Activity 9: Comparing simulation and experiment with R-factors</a></li>
<li class="toctree-l1"><a class="reference internal" href="../Activity10/Activity10.html">Activity 10: Auger Electron Diffraction</a></li>
<li class="toctree-l1"><a class="reference internal" href="../Activity10/Activity10.html">Activity 10: Parallelization and multi-processing in MsSpec</a></li>
<li class="toctree-l1"><a class="reference internal" href="../Activity11/Activity11.html">Activity 11: Spectral radius and convergence</a></li>
<li class="toctree-l1"><a class="reference internal" href="../backmatter.html">Final word</a></li>
</ul>
@ -428,141 +428,138 @@ This is the key to computing the total photodiffraction signal of a <em>substrat
</figcaption>
</figure>
<p>As can be seen in <a class="reference internal" href="#aln-fig5"><span class="std std-numref">Fig. 23</span></a>, the peaks at 32° and 58.5° are well reproduced by the calculation for an Al polarity. Some discreapancies arise between the experimental work and this simulation especially for large polar angles. This may be due to a too small cluster in diameter for the deeper emitters.</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="hll"><span class="linenos"> 1</span><span class="ch">#!/usr/bin/env python</span>
</span><span class="linenos"> 2</span><span class="c1"># coding: utf8</span>
<span class="linenos"> 3</span>
<span class="linenos"> 4</span><span class="kn">from</span><span class="w"> </span><span class="nn">ase.build</span><span class="w"> </span><span class="kn">import</span> <span class="n">bulk</span>
<span class="linenos"> 5</span><span class="kn">import</span><span class="w"> </span><span class="nn">numpy</span><span class="w"> </span><span class="k">as</span><span class="w"> </span><span class="nn">np</span>
<span class="linenos"> 6</span><span class="kn">from</span><span class="w"> </span><span class="nn">msspec.calculator</span><span class="w"> </span><span class="kn">import</span> <span class="n">MSSPEC</span><span class="p">,</span> <span class="n">XRaySource</span>
<span class="linenos"> 7</span><span class="kn">from</span><span class="w"> </span><span class="nn">msspec.utils</span><span class="w"> </span><span class="kn">import</span> <span class="n">hemispherical_cluster</span><span class="p">,</span> <span class="n">get_atom_index</span>
<span class="linenos"> 8</span>
<span class="linenos"> 9</span><span class="k">def</span><span class="w"> </span><span class="nf">create_clusters</span><span class="p">(</span><span class="n">nplanes</span><span class="o">=</span><span class="mi">6</span><span class="p">):</span>
<span class="linenos"> 10</span> <span class="k">def</span><span class="w"> </span><span class="nf">get_AlN_tags_planes</span><span class="p">(</span><span class="n">side</span><span class="p">,</span> <span class="n">emitter</span><span class="p">):</span>
<span class="linenos"> 11</span> <span class="n">AlN</span> <span class="o">=</span> <span class="n">bulk</span><span class="p">(</span><span class="s1">&#39;AlN&#39;</span><span class="p">,</span> <span class="n">crystalstructure</span><span class="o">=</span><span class="s1">&#39;wurtzite&#39;</span><span class="p">,</span> <span class="n">a</span><span class="o">=</span><span class="mf">3.11</span><span class="p">,</span> <span class="n">c</span><span class="o">=</span><span class="mf">4.975</span><span class="p">)</span>
<span class="linenos"> 12</span> <span class="p">[</span><span class="n">atom</span><span class="o">.</span><span class="n">set</span><span class="p">(</span><span class="s1">&#39;tag&#39;</span><span class="p">,</span> <span class="n">i</span><span class="p">)</span> <span class="k">for</span> <span class="n">i</span><span class="p">,</span> <span class="n">atom</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">AlN</span><span class="p">)]</span>
<span class="linenos"> 13</span> <span class="k">if</span> <span class="n">side</span> <span class="o">==</span> <span class="s1">&#39;Al&#39;</span><span class="p">:</span>
<span class="linenos"> 14</span> <span class="n">AlN</span><span class="o">.</span><span class="n">rotate</span><span class="p">([</span><span class="mi">0</span><span class="p">,</span><span class="mi">0</span><span class="p">,</span><span class="mi">1</span><span class="p">],[</span><span class="mi">0</span><span class="p">,</span><span class="mi">0</span><span class="p">,</span><span class="o">-</span><span class="mi">1</span><span class="p">])</span>
<span class="linenos"> 15</span> <span class="n">Al_planes</span> <span class="o">=</span> <span class="nb">range</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="n">nplanes</span><span class="p">,</span> <span class="mi">2</span><span class="p">)</span>
<span class="linenos"> 16</span> <span class="n">N_planes</span> <span class="o">=</span> <span class="nb">range</span><span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="n">nplanes</span><span class="p">,</span> <span class="mi">2</span><span class="p">)</span>
<span class="linenos"> 17</span> <span class="k">else</span><span class="p">:</span>
<span class="linenos"> 18</span> <span class="n">N_planes</span> <span class="o">=</span> <span class="nb">range</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="n">nplanes</span><span class="p">,</span> <span class="mi">2</span><span class="p">)</span>
<span class="linenos"> 19</span> <span class="n">Al_planes</span> <span class="o">=</span> <span class="nb">range</span><span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="n">nplanes</span><span class="p">,</span> <span class="mi">2</span><span class="p">)</span>
<span class="linenos"> 20</span> <span class="k">if</span> <span class="n">emitter</span> <span class="o">==</span> <span class="s1">&#39;Al&#39;</span><span class="p">:</span>
<span class="linenos"> 21</span> <span class="n">tags</span> <span class="o">=</span> <span class="p">[</span><span class="mi">0</span><span class="p">,</span> <span class="mi">2</span><span class="p">]</span>
<span class="linenos"> 22</span> <span class="n">planes</span> <span class="o">=</span> <span class="n">Al_planes</span>
<span class="linenos"> 23</span> <span class="k">else</span><span class="p">:</span>
<span class="linenos"> 24</span> <span class="n">tags</span> <span class="o">=</span> <span class="p">[</span><span class="mi">1</span><span class="p">,</span> <span class="mi">3</span><span class="p">]</span>
<span class="linenos"> 25</span> <span class="n">planes</span> <span class="o">=</span> <span class="n">N_planes</span>
<span class="linenos"> 26</span> <span class="k">return</span> <span class="n">AlN</span><span class="p">,</span> <span class="n">tags</span><span class="p">,</span> <span class="n">planes</span>
<span class="linenos"> 27</span>
<span class="linenos"> 28</span> <span class="n">clusters</span> <span class="o">=</span> <span class="p">[]</span>
<span class="linenos"> 29</span> <span class="k">for</span> <span class="n">side</span> <span class="ow">in</span> <span class="p">(</span><span class="s1">&#39;Al&#39;</span><span class="p">,</span> <span class="s1">&#39;N&#39;</span><span class="p">):</span>
<span class="linenos"> 30</span> <span class="k">for</span> <span class="n">emitter</span> <span class="ow">in</span> <span class="p">(</span><span class="s1">&#39;Al&#39;</span><span class="p">,</span> <span class="s1">&#39;N&#39;</span><span class="p">):</span>
<span class="linenos"> 31</span> <span class="n">AlN</span><span class="p">,</span> <span class="n">tags</span><span class="p">,</span> <span class="n">planes</span> <span class="o">=</span> <span class="n">get_AlN_tags_planes</span><span class="p">(</span><span class="n">side</span><span class="p">,</span> <span class="n">emitter</span><span class="p">)</span>
<span class="linenos"> 32</span> <span class="k">for</span> <span class="n">emitter_tag</span> <span class="ow">in</span> <span class="n">tags</span><span class="p">:</span>
<span class="linenos"> 33</span> <span class="k">for</span> <span class="n">emitter_plane</span> <span class="ow">in</span> <span class="n">planes</span><span class="p">:</span>
<span class="linenos"> 34</span> <span class="n">cluster</span> <span class="o">=</span> <span class="n">hemispherical_cluster</span><span class="p">(</span><span class="n">AlN</span><span class="p">,</span>
<span class="linenos"> 35</span> <span class="n">emitter_tag</span><span class="o">=</span><span class="n">emitter_tag</span><span class="p">,</span>
<span class="linenos"> 36</span> <span class="n">emitter_plane</span><span class="o">=</span><span class="n">emitter_plane</span><span class="p">,</span>
<span class="linenos"> 37</span> <span class="n">planes</span><span class="o">=</span><span class="n">emitter_plane</span><span class="o">+</span><span class="mi">2</span><span class="p">)</span>
<span class="linenos"> 38</span> <span class="n">cluster</span><span class="o">.</span><span class="n">absorber</span> <span class="o">=</span> <span class="n">get_atom_index</span><span class="p">(</span><span class="n">cluster</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">)</span>
<span class="linenos"> 39</span> <span class="n">cluster</span><span class="o">.</span><span class="n">info</span><span class="o">.</span><span class="n">update</span><span class="p">({</span>
<span class="linenos"> 40</span> <span class="s1">&#39;emitter_plane&#39;</span><span class="p">:</span> <span class="n">emitter_plane</span><span class="p">,</span>
<span class="linenos"> 41</span> <span class="s1">&#39;emitter_tag&#39;</span> <span class="p">:</span> <span class="n">emitter_tag</span><span class="p">,</span>
<span class="linenos"> 42</span> <span class="s1">&#39;emitter&#39;</span> <span class="p">:</span> <span class="n">emitter</span><span class="p">,</span>
<span class="linenos"> 43</span> <span class="s1">&#39;side&#39;</span> <span class="p">:</span> <span class="n">side</span><span class="p">,</span>
<span class="linenos"> 44</span> <span class="p">})</span>
<span class="linenos"> 45</span> <span class="n">clusters</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">cluster</span><span class="p">)</span>
<span class="linenos"> 46</span> <span class="nb">print</span><span class="p">(</span><span class="s2">&quot;Added cluster </span><span class="si">{}</span><span class="s2">-side, emitter </span><span class="si">{}</span><span class="s2">(tag </span><span class="si">{:d}</span><span class="s2">) in &quot;</span>
<span class="linenos"> 47</span> <span class="s2">&quot;plane #</span><span class="si">{:d}</span><span class="s2">&quot;</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">side</span><span class="p">,</span> <span class="n">emitter</span><span class="p">,</span> <span class="n">emitter_tag</span><span class="p">,</span>
<span class="linenos"> 48</span> <span class="n">emitter_plane</span><span class="p">))</span>
<span class="linenos"> 49</span> <span class="k">return</span> <span class="n">clusters</span>
<span class="linenos"> 50</span>
<span class="linenos"> 51</span>
<span class="linenos"> 52</span><span class="k">def</span><span class="w"> </span><span class="nf">compute</span><span class="p">(</span><span class="n">clusters</span><span class="p">,</span> <span class="n">theta</span><span class="o">=</span><span class="n">np</span><span class="o">.</span><span class="n">arange</span><span class="p">(</span><span class="o">-</span><span class="mf">20.</span><span class="p">,</span> <span class="mf">80.</span><span class="p">,</span> <span class="mf">1.</span><span class="p">),</span> <span class="n">phi</span><span class="o">=</span><span class="mf">0.</span><span class="p">):</span>
<span class="linenos"> 53</span> <span class="n">data</span> <span class="o">=</span> <span class="kc">None</span>
<span class="linenos"> 54</span> <span class="k">for</span> <span class="n">ic</span><span class="p">,</span> <span class="n">cluster</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">clusters</span><span class="p">):</span>
<span class="linenos"> 55</span> <span class="c1"># Retrieve info from cluster object</span>
<span class="linenos"> 56</span> <span class="n">side</span> <span class="o">=</span> <span class="n">cluster</span><span class="o">.</span><span class="n">info</span><span class="p">[</span><span class="s1">&#39;side&#39;</span><span class="p">]</span>
<span class="linenos"> 57</span> <span class="n">emitter</span> <span class="o">=</span> <span class="n">cluster</span><span class="o">.</span><span class="n">info</span><span class="p">[</span><span class="s1">&#39;emitter&#39;</span><span class="p">]</span>
<span class="linenos"> 58</span> <span class="n">plane</span> <span class="o">=</span> <span class="n">cluster</span><span class="o">.</span><span class="n">info</span><span class="p">[</span><span class="s1">&#39;emitter_plane&#39;</span><span class="p">]</span>
<span class="linenos"> 59</span> <span class="n">tag</span> <span class="o">=</span> <span class="n">cluster</span><span class="o">.</span><span class="n">info</span><span class="p">[</span><span class="s1">&#39;emitter_tag&#39;</span><span class="p">]</span>
<span class="linenos"> 60</span>
<span class="linenos"> 61</span> <span class="c1"># Set the level and the kinetic energy</span>
<span class="linenos"> 62</span> <span class="k">if</span> <span class="n">emitter</span> <span class="o">==</span> <span class="s1">&#39;Al&#39;</span><span class="p">:</span>
<span class="linenos"> 63</span> <span class="n">level</span> <span class="o">=</span> <span class="s1">&#39;2p&#39;</span>
<span class="linenos"> 64</span> <span class="n">ke</span> <span class="o">=</span> <span class="mf">1407.</span>
<span class="linenos"> 65</span> <span class="k">elif</span> <span class="n">emitter</span> <span class="o">==</span> <span class="s1">&#39;N&#39;</span><span class="p">:</span>
<span class="linenos"> 66</span> <span class="n">level</span> <span class="o">=</span> <span class="s1">&#39;1s&#39;</span>
<span class="linenos"> 67</span> <span class="n">ke</span> <span class="o">=</span> <span class="mf">1083.</span>
<span class="linenos"> 68</span>
<span class="linenos"> 69</span> <span class="n">calc</span> <span class="o">=</span> <span class="n">MSSPEC</span><span class="p">(</span><span class="n">spectroscopy</span><span class="o">=</span><span class="s1">&#39;PED&#39;</span><span class="p">,</span> <span class="n">algorithm</span><span class="o">=</span><span class="s1">&#39;expansion&#39;</span><span class="p">)</span>
<span class="linenos"> 70</span>
<span class="linenos"> 71</span> <span class="n">calc</span><span class="o">.</span><span class="n">source_parameters</span><span class="o">.</span><span class="n">energy</span> <span class="o">=</span> <span class="n">XRaySource</span><span class="o">.</span><span class="n">AL_KALPHA</span>
<span class="linenos"> 72</span> <span class="n">calc</span><span class="o">.</span><span class="n">source_parameters</span><span class="o">.</span><span class="n">theta</span> <span class="o">=</span> <span class="o">-</span><span class="mi">35</span>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="linenos"> 1</span><span class="kn">from</span><span class="w"> </span><span class="nn">ase.build</span><span class="w"> </span><span class="kn">import</span> <span class="n">bulk</span>
<span class="linenos"> 2</span><span class="kn">import</span><span class="w"> </span><span class="nn">numpy</span><span class="w"> </span><span class="k">as</span><span class="w"> </span><span class="nn">np</span>
<span class="linenos"> 3</span><span class="kn">from</span><span class="w"> </span><span class="nn">msspec.calculator</span><span class="w"> </span><span class="kn">import</span> <span class="n">MSSPEC</span><span class="p">,</span> <span class="n">XRaySource</span>
<span class="linenos"> 4</span><span class="kn">from</span><span class="w"> </span><span class="nn">msspec.utils</span><span class="w"> </span><span class="kn">import</span> <span class="n">hemispherical_cluster</span><span class="p">,</span> <span class="n">get_atom_index</span>
<span class="linenos"> 5</span>
<span class="linenos"> 6</span><span class="k">def</span><span class="w"> </span><span class="nf">create_clusters</span><span class="p">(</span><span class="n">nplanes</span><span class="o">=</span><span class="mi">6</span><span class="p">):</span>
<span class="linenos"> 7</span> <span class="k">def</span><span class="w"> </span><span class="nf">get_AlN_tags_planes</span><span class="p">(</span><span class="n">side</span><span class="p">,</span> <span class="n">emitter</span><span class="p">):</span>
<span class="hll"><span class="linenos"> 8</span> <span class="n">AlN</span> <span class="o">=</span> <span class="n">bulk</span><span class="p">(</span><span class="s1">&#39;AlN&#39;</span><span class="p">,</span> <span class="n">crystalstructure</span><span class="o">=</span><span class="s1">&#39;wurtzite&#39;</span><span class="p">,</span> <span class="n">a</span><span class="o">=</span><span class="mf">3.11</span><span class="p">,</span> <span class="n">c</span><span class="o">=</span><span class="mf">4.975</span><span class="p">)</span>
</span><span class="linenos"> 9</span> <span class="p">[</span><span class="n">atom</span><span class="o">.</span><span class="n">set</span><span class="p">(</span><span class="s1">&#39;tag&#39;</span><span class="p">,</span> <span class="n">i</span><span class="p">)</span> <span class="k">for</span> <span class="n">i</span><span class="p">,</span> <span class="n">atom</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">AlN</span><span class="p">)]</span>
<span class="linenos"> 10</span> <span class="k">if</span> <span class="n">side</span> <span class="o">==</span> <span class="s1">&#39;Al&#39;</span><span class="p">:</span>
<span class="linenos"> 11</span> <span class="n">AlN</span><span class="o">.</span><span class="n">rotate</span><span class="p">([</span><span class="mi">0</span><span class="p">,</span><span class="mi">0</span><span class="p">,</span><span class="mi">1</span><span class="p">],[</span><span class="mi">0</span><span class="p">,</span><span class="mi">0</span><span class="p">,</span><span class="o">-</span><span class="mi">1</span><span class="p">])</span>
<span class="linenos"> 12</span> <span class="n">Al_planes</span> <span class="o">=</span> <span class="nb">range</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="n">nplanes</span><span class="p">,</span> <span class="mi">2</span><span class="p">)</span>
<span class="linenos"> 13</span> <span class="n">N_planes</span> <span class="o">=</span> <span class="nb">range</span><span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="n">nplanes</span><span class="p">,</span> <span class="mi">2</span><span class="p">)</span>
<span class="linenos"> 14</span> <span class="k">else</span><span class="p">:</span>
<span class="linenos"> 15</span> <span class="n">N_planes</span> <span class="o">=</span> <span class="nb">range</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="n">nplanes</span><span class="p">,</span> <span class="mi">2</span><span class="p">)</span>
<span class="linenos"> 16</span> <span class="n">Al_planes</span> <span class="o">=</span> <span class="nb">range</span><span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="n">nplanes</span><span class="p">,</span> <span class="mi">2</span><span class="p">)</span>
<span class="linenos"> 17</span> <span class="k">if</span> <span class="n">emitter</span> <span class="o">==</span> <span class="s1">&#39;Al&#39;</span><span class="p">:</span>
<span class="linenos"> 18</span> <span class="n">tags</span> <span class="o">=</span> <span class="p">[</span><span class="mi">0</span><span class="p">,</span> <span class="mi">2</span><span class="p">]</span>
<span class="linenos"> 19</span> <span class="n">planes</span> <span class="o">=</span> <span class="n">Al_planes</span>
<span class="linenos"> 20</span> <span class="k">else</span><span class="p">:</span>
<span class="linenos"> 21</span> <span class="n">tags</span> <span class="o">=</span> <span class="p">[</span><span class="mi">1</span><span class="p">,</span> <span class="mi">3</span><span class="p">]</span>
<span class="linenos"> 22</span> <span class="n">planes</span> <span class="o">=</span> <span class="n">N_planes</span>
<span class="linenos"> 23</span> <span class="k">return</span> <span class="n">AlN</span><span class="p">,</span> <span class="n">tags</span><span class="p">,</span> <span class="n">planes</span>
<span class="linenos"> 24</span>
<span class="linenos"> 25</span> <span class="n">clusters</span> <span class="o">=</span> <span class="p">[]</span>
<span class="linenos"> 26</span> <span class="k">for</span> <span class="n">side</span> <span class="ow">in</span> <span class="p">(</span><span class="s1">&#39;Al&#39;</span><span class="p">,</span> <span class="s1">&#39;N&#39;</span><span class="p">):</span>
<span class="linenos"> 27</span> <span class="k">for</span> <span class="n">emitter</span> <span class="ow">in</span> <span class="p">(</span><span class="s1">&#39;Al&#39;</span><span class="p">,</span> <span class="s1">&#39;N&#39;</span><span class="p">):</span>
<span class="linenos"> 28</span> <span class="n">AlN</span><span class="p">,</span> <span class="n">tags</span><span class="p">,</span> <span class="n">planes</span> <span class="o">=</span> <span class="n">get_AlN_tags_planes</span><span class="p">(</span><span class="n">side</span><span class="p">,</span> <span class="n">emitter</span><span class="p">)</span>
<span class="linenos"> 29</span> <span class="k">for</span> <span class="n">emitter_tag</span> <span class="ow">in</span> <span class="n">tags</span><span class="p">:</span>
<span class="linenos"> 30</span> <span class="k">for</span> <span class="n">emitter_plane</span> <span class="ow">in</span> <span class="n">planes</span><span class="p">:</span>
<span class="hll"><span class="linenos"> 31</span> <span class="n">cluster</span> <span class="o">=</span> <span class="n">hemispherical_cluster</span><span class="p">(</span><span class="n">AlN</span><span class="p">,</span>
</span><span class="hll"><span class="linenos"> 32</span> <span class="n">emitter_tag</span><span class="o">=</span><span class="n">emitter_tag</span><span class="p">,</span>
</span><span class="hll"><span class="linenos"> 33</span> <span class="n">emitter_plane</span><span class="o">=</span><span class="n">emitter_plane</span><span class="p">,</span>
</span><span class="hll"><span class="linenos"> 34</span> <span class="n">planes</span><span class="o">=</span><span class="n">emitter_plane</span><span class="o">+</span><span class="mi">2</span><span class="p">)</span>
</span><span class="linenos"> 35</span> <span class="n">cluster</span><span class="o">.</span><span class="n">absorber</span> <span class="o">=</span> <span class="n">get_atom_index</span><span class="p">(</span><span class="n">cluster</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">)</span>
<span class="linenos"> 36</span> <span class="n">cluster</span><span class="o">.</span><span class="n">info</span><span class="o">.</span><span class="n">update</span><span class="p">({</span>
<span class="linenos"> 37</span> <span class="s1">&#39;emitter_plane&#39;</span><span class="p">:</span> <span class="n">emitter_plane</span><span class="p">,</span>
<span class="linenos"> 38</span> <span class="s1">&#39;emitter_tag&#39;</span> <span class="p">:</span> <span class="n">emitter_tag</span><span class="p">,</span>
<span class="linenos"> 39</span> <span class="s1">&#39;emitter&#39;</span> <span class="p">:</span> <span class="n">emitter</span><span class="p">,</span>
<span class="linenos"> 40</span> <span class="s1">&#39;side&#39;</span> <span class="p">:</span> <span class="n">side</span><span class="p">,</span>
<span class="linenos"> 41</span> <span class="p">})</span>
<span class="linenos"> 42</span> <span class="n">clusters</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">cluster</span><span class="p">)</span>
<span class="linenos"> 43</span> <span class="nb">print</span><span class="p">(</span><span class="s2">&quot;Added cluster </span><span class="si">{}</span><span class="s2">-side, emitter </span><span class="si">{}</span><span class="s2">(tag </span><span class="si">{:d}</span><span class="s2">) in &quot;</span>
<span class="linenos"> 44</span> <span class="s2">&quot;plane #</span><span class="si">{:d}</span><span class="s2">&quot;</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">side</span><span class="p">,</span> <span class="n">emitter</span><span class="p">,</span> <span class="n">emitter_tag</span><span class="p">,</span>
<span class="linenos"> 45</span> <span class="n">emitter_plane</span><span class="p">))</span>
<span class="linenos"> 46</span> <span class="k">return</span> <span class="n">clusters</span>
<span class="linenos"> 47</span>
<span class="linenos"> 48</span>
<span class="linenos"> 49</span><span class="k">def</span><span class="w"> </span><span class="nf">compute</span><span class="p">(</span><span class="n">clusters</span><span class="p">,</span> <span class="n">theta</span><span class="o">=</span><span class="n">np</span><span class="o">.</span><span class="n">arange</span><span class="p">(</span><span class="o">-</span><span class="mf">20.</span><span class="p">,</span> <span class="mf">80.</span><span class="p">,</span> <span class="mf">1.</span><span class="p">),</span> <span class="n">phi</span><span class="o">=</span><span class="mf">0.</span><span class="p">):</span>
<span class="linenos"> 50</span> <span class="n">data</span> <span class="o">=</span> <span class="kc">None</span>
<span class="linenos"> 51</span> <span class="k">for</span> <span class="n">ic</span><span class="p">,</span> <span class="n">cluster</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">clusters</span><span class="p">):</span>
<span class="linenos"> 52</span> <span class="c1"># Retrieve info from cluster object</span>
<span class="linenos"> 53</span> <span class="n">side</span> <span class="o">=</span> <span class="n">cluster</span><span class="o">.</span><span class="n">info</span><span class="p">[</span><span class="s1">&#39;side&#39;</span><span class="p">]</span>
<span class="linenos"> 54</span> <span class="n">emitter</span> <span class="o">=</span> <span class="n">cluster</span><span class="o">.</span><span class="n">info</span><span class="p">[</span><span class="s1">&#39;emitter&#39;</span><span class="p">]</span>
<span class="linenos"> 55</span> <span class="n">plane</span> <span class="o">=</span> <span class="n">cluster</span><span class="o">.</span><span class="n">info</span><span class="p">[</span><span class="s1">&#39;emitter_plane&#39;</span><span class="p">]</span>
<span class="linenos"> 56</span> <span class="n">tag</span> <span class="o">=</span> <span class="n">cluster</span><span class="o">.</span><span class="n">info</span><span class="p">[</span><span class="s1">&#39;emitter_tag&#39;</span><span class="p">]</span>
<span class="linenos"> 57</span>
<span class="linenos"> 58</span> <span class="c1"># Set the level and the kinetic energy</span>
<span class="linenos"> 59</span> <span class="k">if</span> <span class="n">emitter</span> <span class="o">==</span> <span class="s1">&#39;Al&#39;</span><span class="p">:</span>
<span class="hll"><span class="linenos"> 60</span> <span class="n">level</span> <span class="o">=</span> <span class="s1">&#39;2p&#39;</span>
</span><span class="hll"><span class="linenos"> 61</span> <span class="n">ke</span> <span class="o">=</span> <span class="mf">1407.</span>
</span><span class="linenos"> 62</span> <span class="k">elif</span> <span class="n">emitter</span> <span class="o">==</span> <span class="s1">&#39;N&#39;</span><span class="p">:</span>
<span class="hll"><span class="linenos"> 63</span> <span class="n">level</span> <span class="o">=</span> <span class="s1">&#39;1s&#39;</span>
</span><span class="hll"><span class="linenos"> 64</span> <span class="n">ke</span> <span class="o">=</span> <span class="mf">1083.</span>
</span><span class="linenos"> 65</span>
<span class="hll"><span class="linenos"> 66</span> <span class="n">calc</span> <span class="o">=</span> <span class="n">MSSPEC</span><span class="p">(</span><span class="n">spectroscopy</span><span class="o">=</span><span class="s1">&#39;PED&#39;</span><span class="p">,</span> <span class="n">algorithm</span><span class="o">=</span><span class="s1">&#39;expansion&#39;</span><span class="p">)</span>
</span><span class="linenos"> 67</span>
<span class="hll"><span class="linenos"> 68</span> <span class="n">calc</span><span class="o">.</span><span class="n">source_parameters</span><span class="o">.</span><span class="n">energy</span> <span class="o">=</span> <span class="n">XRaySource</span><span class="o">.</span><span class="n">AL_KALPHA</span>
</span><span class="hll"><span class="linenos"> 69</span> <span class="n">calc</span><span class="o">.</span><span class="n">source_parameters</span><span class="o">.</span><span class="n">theta</span> <span class="o">=</span> <span class="o">-</span><span class="mi">35</span>
</span><span class="linenos"> 70</span>
<span class="hll"><span class="linenos"> 71</span> <span class="n">calc</span><span class="o">.</span><span class="n">detector_parameters</span><span class="o">.</span><span class="n">angular_acceptance</span> <span class="o">=</span> <span class="mf">4.</span>
</span><span class="linenos"> 72</span> <span class="n">calc</span><span class="o">.</span><span class="n">detector_parameters</span><span class="o">.</span><span class="n">average_sampling</span> <span class="o">=</span> <span class="s1">&#39;medium&#39;</span>
<span class="linenos"> 73</span>
<span class="linenos"> 74</span> <span class="n">calc</span><span class="o">.</span><span class="n">detector_parameters</span><span class="o">.</span><span class="n">angular_acceptance</span> <span class="o">=</span> <span class="mf">4.</span>
<span class="linenos"> 75</span> <span class="n">calc</span><span class="o">.</span><span class="n">detector_parameters</span><span class="o">.</span><span class="n">average_sampling</span> <span class="o">=</span> <span class="s1">&#39;medium&#39;</span>
<span class="linenos"> 76</span>
<span class="linenos"> 77</span> <span class="n">calc</span><span class="o">.</span><span class="n">calculation_parameters</span><span class="o">.</span><span class="n">scattering_order</span> <span class="o">=</span> <span class="nb">max</span><span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="nb">min</span><span class="p">(</span><span class="mi">4</span><span class="p">,</span> <span class="n">plane</span><span class="p">))</span>
<span class="linenos"> 78</span> <span class="n">calc</span><span class="o">.</span><span class="n">calculation_parameters</span><span class="o">.</span><span class="n">path_filtering</span> <span class="o">=</span> <span class="s1">&#39;forward_scattering&#39;</span>
<span class="linenos"> 79</span> <span class="n">calc</span><span class="o">.</span><span class="n">calculation_parameters</span><span class="o">.</span><span class="n">off_cone_events</span> <span class="o">=</span> <span class="mi">1</span>
<span class="linenos"> 80</span> <span class="p">[</span><span class="n">a</span><span class="o">.</span><span class="n">set</span><span class="p">(</span><span class="s1">&#39;forward_angle&#39;</span><span class="p">,</span> <span class="mf">30.</span><span class="p">)</span> <span class="k">for</span> <span class="n">a</span> <span class="ow">in</span> <span class="n">cluster</span><span class="p">]</span>
<span class="linenos"> 81</span>
<span class="linenos"> 82</span> <span class="n">calc</span><span class="o">.</span><span class="n">set_atoms</span><span class="p">(</span><span class="n">cluster</span><span class="p">)</span>
<span class="linenos"> 83</span>
<span class="linenos"> 84</span> <span class="n">data</span> <span class="o">=</span> <span class="n">calc</span><span class="o">.</span><span class="n">get_theta_scan</span><span class="p">(</span><span class="n">level</span><span class="o">=</span><span class="n">level</span><span class="p">,</span> <span class="n">theta</span><span class="o">=</span><span class="n">theta</span><span class="p">,</span> <span class="n">phi</span><span class="o">=</span><span class="n">phi</span><span class="p">,</span>
<span class="linenos"> 85</span> <span class="n">kinetic_energy</span><span class="o">=</span><span class="n">ke</span><span class="p">,</span> <span class="n">data</span><span class="o">=</span><span class="n">data</span><span class="p">)</span>
<span class="linenos"> 86</span> <span class="n">dset</span> <span class="o">=</span> <span class="n">data</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span>
<span class="linenos"> 87</span> <span class="n">dset</span><span class="o">.</span><span class="n">title</span> <span class="o">=</span> <span class="s2">&quot;</span><span class="se">\&#39;</span><span class="si">{}</span><span class="se">\&#39;</span><span class="s2"> side - </span><span class="si">{}</span><span class="s2">(</span><span class="si">{}</span><span class="s2">) tag #</span><span class="si">{:d}</span><span class="s2">, plane #</span><span class="si">{:d}</span><span class="s2">&quot;</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
<span class="linenos"> 88</span> <span class="n">side</span><span class="p">,</span> <span class="n">emitter</span><span class="p">,</span> <span class="n">level</span><span class="p">,</span> <span class="n">tag</span><span class="p">,</span> <span class="n">plane</span><span class="p">)</span>
<span class="linenos"> 74</span> <span class="n">calc</span><span class="o">.</span><span class="n">calculation_parameters</span><span class="o">.</span><span class="n">scattering_order</span> <span class="o">=</span> <span class="nb">max</span><span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="nb">min</span><span class="p">(</span><span class="mi">4</span><span class="p">,</span> <span class="n">plane</span><span class="p">))</span>
<span class="linenos"> 75</span> <span class="n">calc</span><span class="o">.</span><span class="n">calculation_parameters</span><span class="o">.</span><span class="n">path_filtering</span> <span class="o">=</span> <span class="s1">&#39;forward_scattering&#39;</span>
<span class="linenos"> 76</span> <span class="n">calc</span><span class="o">.</span><span class="n">calculation_parameters</span><span class="o">.</span><span class="n">off_cone_events</span> <span class="o">=</span> <span class="mi">1</span>
<span class="linenos"> 77</span> <span class="p">[</span><span class="n">a</span><span class="o">.</span><span class="n">set</span><span class="p">(</span><span class="s1">&#39;forward_angle&#39;</span><span class="p">,</span> <span class="mf">30.</span><span class="p">)</span> <span class="k">for</span> <span class="n">a</span> <span class="ow">in</span> <span class="n">cluster</span><span class="p">]</span>
<span class="linenos"> 78</span>
<span class="linenos"> 79</span> <span class="n">calc</span><span class="o">.</span><span class="n">set_atoms</span><span class="p">(</span><span class="n">cluster</span><span class="p">)</span>
<span class="linenos"> 80</span>
<span class="linenos"> 81</span> <span class="n">data</span> <span class="o">=</span> <span class="n">calc</span><span class="o">.</span><span class="n">get_theta_scan</span><span class="p">(</span><span class="n">level</span><span class="o">=</span><span class="n">level</span><span class="p">,</span> <span class="n">theta</span><span class="o">=</span><span class="n">theta</span><span class="p">,</span> <span class="n">phi</span><span class="o">=</span><span class="n">phi</span><span class="p">,</span>
<span class="linenos"> 82</span> <span class="n">kinetic_energy</span><span class="o">=</span><span class="n">ke</span><span class="p">,</span> <span class="n">data</span><span class="o">=</span><span class="n">data</span><span class="p">)</span>
<span class="linenos"> 83</span> <span class="n">dset</span> <span class="o">=</span> <span class="n">data</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span>
<span class="linenos"> 84</span> <span class="n">dset</span><span class="o">.</span><span class="n">title</span> <span class="o">=</span> <span class="s2">&quot;</span><span class="se">\&#39;</span><span class="si">{}</span><span class="se">\&#39;</span><span class="s2"> side - </span><span class="si">{}</span><span class="s2">(</span><span class="si">{}</span><span class="s2">) tag #</span><span class="si">{:d}</span><span class="s2">, plane #</span><span class="si">{:d}</span><span class="s2">&quot;</span><span class="o">.</span><span class="n">format</span><span class="p">(</span>
<span class="linenos"> 85</span> <span class="n">side</span><span class="p">,</span> <span class="n">emitter</span><span class="p">,</span> <span class="n">level</span><span class="p">,</span> <span class="n">tag</span><span class="p">,</span> <span class="n">plane</span><span class="p">)</span>
<span class="linenos"> 86</span>
<span class="linenos"> 87</span> <span class="k">return</span> <span class="n">data</span>
<span class="linenos"> 88</span>
<span class="linenos"> 89</span>
<span class="linenos"> 90</span> <span class="k">return</span> <span class="n">data</span>
<span class="linenos"> 91</span>
<span class="linenos"> 92</span>
<span class="linenos"> 93</span><span class="k">def</span><span class="w"> </span><span class="nf">analysis</span><span class="p">(</span><span class="n">data</span><span class="p">):</span>
<span class="linenos"> 94</span> <span class="n">tmp_data</span> <span class="o">=</span> <span class="p">{}</span>
<span class="linenos"> 95</span> <span class="k">for</span> <span class="n">dset</span> <span class="ow">in</span> <span class="n">data</span><span class="p">:</span>
<span class="linenos"> 96</span> <span class="n">info</span> <span class="o">=</span> <span class="n">dset</span><span class="o">.</span><span class="n">get_cluster</span><span class="p">()</span><span class="o">.</span><span class="n">info</span>
<span class="linenos"> 97</span> <span class="n">side</span> <span class="o">=</span> <span class="n">info</span><span class="p">[</span><span class="s1">&#39;side&#39;</span><span class="p">]</span>
<span class="linenos"> 98</span> <span class="n">emitter</span> <span class="o">=</span> <span class="n">info</span><span class="p">[</span><span class="s1">&#39;emitter&#39;</span><span class="p">]</span>
<span class="linenos"> 99</span> <span class="k">try</span><span class="p">:</span>
<span class="linenos">100</span> <span class="n">key</span> <span class="o">=</span> <span class="s1">&#39;</span><span class="si">{}</span><span class="s1">_</span><span class="si">{}</span><span class="s1">&#39;</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">side</span><span class="p">,</span> <span class="n">emitter</span><span class="p">)</span>
<span class="linenos">101</span> <span class="n">tmp_data</span><span class="p">[</span><span class="n">key</span><span class="p">]</span> <span class="o">+=</span> <span class="n">dset</span><span class="o">.</span><span class="n">cross_section</span>
<span class="linenos">102</span> <span class="k">except</span> <span class="ne">KeyError</span><span class="p">:</span>
<span class="linenos">103</span> <span class="n">tmp_data</span><span class="p">[</span><span class="n">key</span><span class="p">]</span> <span class="o">=</span> <span class="n">dset</span><span class="o">.</span><span class="n">cross_section</span><span class="o">.</span><span class="n">copy</span><span class="p">()</span>
<span class="linenos">104</span>
<span class="linenos">105</span> <span class="n">tmp_data</span><span class="p">[</span><span class="s1">&#39;theta&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">dset</span><span class="o">.</span><span class="n">theta</span><span class="o">.</span><span class="n">copy</span><span class="p">()</span>
<span class="linenos">106</span> <span class="n">tmp_data</span><span class="p">[</span><span class="s1">&#39;Al_side&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">tmp_data</span><span class="p">[</span><span class="s1">&#39;Al_Al&#39;</span><span class="p">]</span> <span class="o">/</span> <span class="n">tmp_data</span><span class="p">[</span><span class="s1">&#39;Al_N&#39;</span><span class="p">]</span>
<span class="linenos">107</span> <span class="n">tmp_data</span><span class="p">[</span><span class="s1">&#39;N_side&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">tmp_data</span><span class="p">[</span><span class="s1">&#39;N_Al&#39;</span><span class="p">]</span> <span class="o">/</span> <span class="n">tmp_data</span><span class="p">[</span><span class="s1">&#39;N_N&#39;</span><span class="p">]</span>
<span class="linenos">108</span>
<span class="linenos">109</span> <span class="c1"># now add all columns</span>
<span class="linenos">110</span> <span class="n">substrate_dset</span> <span class="o">=</span> <span class="n">data</span><span class="o">.</span><span class="n">add_dset</span><span class="p">(</span><span class="s1">&#39;Total substrate signal&#39;</span><span class="p">)</span>
<span class="linenos">111</span> <span class="n">substrate_dset</span><span class="o">.</span><span class="n">add_columns</span><span class="p">(</span><span class="o">**</span><span class="n">tmp_data</span><span class="p">)</span>
<span class="linenos">112</span>
<span class="linenos">113</span> <span class="n">view</span> <span class="o">=</span> <span class="n">substrate_dset</span><span class="o">.</span><span class="n">add_view</span><span class="p">(</span><span class="s1">&#39;Ratios&#39;</span><span class="p">,</span>
<span class="linenos">114</span> <span class="n">title</span><span class="o">=</span><span class="sa">r</span><span class="s1">&#39;Al(2p)/N(1s) ratios on both polar &#39;</span>
<span class="linenos">115</span> <span class="sa">r</span><span class="s1">&#39;sides of AlN in the (10$\bar</span><span class="si">{1}</span><span class="s1">$0) &#39;</span>
<span class="linenos">116</span> <span class="sa">r</span><span class="s1">&#39;azimuthal plane&#39;</span><span class="p">,</span>
<span class="linenos">117</span> <span class="n">xlabel</span><span class="o">=</span><span class="sa">r</span><span class="s1">&#39;$\Theta (\degree$)&#39;</span><span class="p">,</span>
<span class="linenos">118</span> <span class="n">ylabel</span><span class="o">=</span><span class="s1">&#39;Intenisty ratio&#39;</span><span class="p">)</span>
<span class="linenos">119</span> <span class="n">view</span><span class="o">.</span><span class="n">select</span><span class="p">(</span><span class="s1">&#39;theta&#39;</span><span class="p">,</span> <span class="s1">&#39;Al_side&#39;</span><span class="p">,</span> <span class="n">legend</span><span class="o">=</span><span class="s1">&#39;Al side&#39;</span><span class="p">,</span>
<span class="linenos">120</span> <span class="n">where</span><span class="o">=</span><span class="s2">&quot;theta &gt;= 0 and theta &lt;=70&quot;</span><span class="p">)</span>
<span class="linenos">121</span> <span class="n">view</span><span class="o">.</span><span class="n">select</span><span class="p">(</span><span class="s1">&#39;theta&#39;</span><span class="p">,</span> <span class="s1">&#39;N_side&#39;</span><span class="p">,</span> <span class="n">legend</span><span class="o">=</span><span class="s1">&#39;N side&#39;</span><span class="p">,</span>
<span class="linenos">122</span> <span class="n">where</span><span class="o">=</span><span class="s2">&quot;theta &gt;= 0 and theta &lt;=70&quot;</span><span class="p">)</span>
<span class="linenos">123</span> <span class="n">view</span><span class="o">.</span><span class="n">set_plot_options</span><span class="p">(</span><span class="n">autoscale</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
<span class="linenos"> 90</span><span class="k">def</span><span class="w"> </span><span class="nf">analysis</span><span class="p">(</span><span class="n">data</span><span class="p">):</span>
<span class="linenos"> 91</span> <span class="n">tmp_data</span> <span class="o">=</span> <span class="p">{}</span>
<span class="linenos"> 92</span> <span class="k">for</span> <span class="n">dset</span> <span class="ow">in</span> <span class="n">data</span><span class="p">:</span>
<span class="linenos"> 93</span> <span class="n">info</span> <span class="o">=</span> <span class="n">dset</span><span class="o">.</span><span class="n">get_cluster</span><span class="p">()</span><span class="o">.</span><span class="n">info</span>
<span class="linenos"> 94</span> <span class="n">side</span> <span class="o">=</span> <span class="n">info</span><span class="p">[</span><span class="s1">&#39;side&#39;</span><span class="p">]</span>
<span class="linenos"> 95</span> <span class="n">emitter</span> <span class="o">=</span> <span class="n">info</span><span class="p">[</span><span class="s1">&#39;emitter&#39;</span><span class="p">]</span>
<span class="linenos"> 96</span> <span class="k">try</span><span class="p">:</span>
<span class="linenos"> 97</span> <span class="n">key</span> <span class="o">=</span> <span class="s1">&#39;</span><span class="si">{}</span><span class="s1">_</span><span class="si">{}</span><span class="s1">&#39;</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">side</span><span class="p">,</span> <span class="n">emitter</span><span class="p">)</span>
<span class="linenos"> 98</span> <span class="n">tmp_data</span><span class="p">[</span><span class="n">key</span><span class="p">]</span> <span class="o">+=</span> <span class="n">dset</span><span class="o">.</span><span class="n">cross_section</span>
<span class="linenos"> 99</span> <span class="k">except</span> <span class="ne">KeyError</span><span class="p">:</span>
<span class="linenos">100</span> <span class="n">tmp_data</span><span class="p">[</span><span class="n">key</span><span class="p">]</span> <span class="o">=</span> <span class="n">dset</span><span class="o">.</span><span class="n">cross_section</span><span class="o">.</span><span class="n">copy</span><span class="p">()</span>
<span class="linenos">101</span>
<span class="linenos">102</span> <span class="n">tmp_data</span><span class="p">[</span><span class="s1">&#39;theta&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">dset</span><span class="o">.</span><span class="n">theta</span><span class="o">.</span><span class="n">copy</span><span class="p">()</span>
<span class="linenos">103</span> <span class="n">tmp_data</span><span class="p">[</span><span class="s1">&#39;Al_side&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">tmp_data</span><span class="p">[</span><span class="s1">&#39;Al_Al&#39;</span><span class="p">]</span> <span class="o">/</span> <span class="n">tmp_data</span><span class="p">[</span><span class="s1">&#39;Al_N&#39;</span><span class="p">]</span>
<span class="linenos">104</span> <span class="n">tmp_data</span><span class="p">[</span><span class="s1">&#39;N_side&#39;</span><span class="p">]</span> <span class="o">=</span> <span class="n">tmp_data</span><span class="p">[</span><span class="s1">&#39;N_Al&#39;</span><span class="p">]</span> <span class="o">/</span> <span class="n">tmp_data</span><span class="p">[</span><span class="s1">&#39;N_N&#39;</span><span class="p">]</span>
<span class="linenos">105</span>
<span class="linenos">106</span> <span class="c1"># now add all columns</span>
<span class="linenos">107</span> <span class="n">substrate_dset</span> <span class="o">=</span> <span class="n">data</span><span class="o">.</span><span class="n">add_dset</span><span class="p">(</span><span class="s1">&#39;Total substrate signal&#39;</span><span class="p">)</span>
<span class="linenos">108</span> <span class="n">substrate_dset</span><span class="o">.</span><span class="n">add_columns</span><span class="p">(</span><span class="o">**</span><span class="n">tmp_data</span><span class="p">)</span>
<span class="linenos">109</span>
<span class="linenos">110</span> <span class="n">view</span> <span class="o">=</span> <span class="n">substrate_dset</span><span class="o">.</span><span class="n">add_view</span><span class="p">(</span><span class="s1">&#39;Ratios&#39;</span><span class="p">,</span>
<span class="linenos">111</span> <span class="n">title</span><span class="o">=</span><span class="sa">r</span><span class="s1">&#39;Al(2p)/N(1s) ratios on both polar &#39;</span>
<span class="linenos">112</span> <span class="sa">r</span><span class="s1">&#39;sides of AlN in the (10$\bar</span><span class="si">{1}</span><span class="s1">$0) &#39;</span>
<span class="linenos">113</span> <span class="sa">r</span><span class="s1">&#39;azimuthal plane&#39;</span><span class="p">,</span>
<span class="linenos">114</span> <span class="n">xlabel</span><span class="o">=</span><span class="sa">r</span><span class="s1">&#39;$\Theta (\degree$)&#39;</span><span class="p">,</span>
<span class="linenos">115</span> <span class="n">ylabel</span><span class="o">=</span><span class="s1">&#39;Intenisty ratio&#39;</span><span class="p">)</span>
<span class="linenos">116</span> <span class="n">view</span><span class="o">.</span><span class="n">select</span><span class="p">(</span><span class="s1">&#39;theta&#39;</span><span class="p">,</span> <span class="s1">&#39;Al_side&#39;</span><span class="p">,</span> <span class="n">legend</span><span class="o">=</span><span class="s1">&#39;Al side&#39;</span><span class="p">,</span>
<span class="linenos">117</span> <span class="n">where</span><span class="o">=</span><span class="s2">&quot;theta &gt;= 0 and theta &lt;=70&quot;</span><span class="p">)</span>
<span class="linenos">118</span> <span class="n">view</span><span class="o">.</span><span class="n">select</span><span class="p">(</span><span class="s1">&#39;theta&#39;</span><span class="p">,</span> <span class="s1">&#39;N_side&#39;</span><span class="p">,</span> <span class="n">legend</span><span class="o">=</span><span class="s1">&#39;N side&#39;</span><span class="p">,</span>
<span class="linenos">119</span> <span class="n">where</span><span class="o">=</span><span class="s2">&quot;theta &gt;= 0 and theta &lt;=70&quot;</span><span class="p">)</span>
<span class="linenos">120</span> <span class="n">view</span><span class="o">.</span><span class="n">set_plot_options</span><span class="p">(</span><span class="n">autoscale</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
<span class="linenos">121</span>
<span class="linenos">122</span> <span class="k">return</span> <span class="n">data</span>
<span class="linenos">123</span>
<span class="linenos">124</span>
<span class="linenos">125</span> <span class="k">return</span> <span class="n">data</span>
<span class="linenos">126</span>
<span class="linenos">127</span>
<span class="linenos">128</span><span class="n">clusters</span> <span class="o">=</span> <span class="n">create_clusters</span><span class="p">()</span>
<span class="linenos">129</span><span class="k">for</span> <span class="n">cluster</span> <span class="ow">in</span> <span class="n">clusters</span><span class="p">:</span>
<span class="linenos">130</span> <span class="n">cluster</span><span class="o">.</span><span class="n">edit</span><span class="p">()</span>
<span class="linenos">131</span><span class="n">exit</span><span class="p">()</span>
<span class="linenos">132</span><span class="n">data</span> <span class="o">=</span> <span class="n">compute</span><span class="p">(</span><span class="n">clusters</span><span class="p">)</span>
<span class="linenos">133</span><span class="n">data</span> <span class="o">=</span> <span class="n">analysis</span><span class="p">(</span><span class="n">data</span><span class="p">)</span>
<span class="linenos">134</span><span class="n">data</span><span class="o">.</span><span class="n">view</span><span class="p">()</span>
<span class="linenos">135</span>
<span class="linenos">125</span><span class="n">clusters</span> <span class="o">=</span> <span class="n">create_clusters</span><span class="p">()</span>
<span class="linenos">126</span><span class="k">for</span> <span class="n">cluster</span> <span class="ow">in</span> <span class="n">clusters</span><span class="p">:</span>
<span class="linenos">127</span> <span class="n">cluster</span><span class="o">.</span><span class="n">edit</span><span class="p">()</span>
<span class="linenos">128</span><span class="n">exit</span><span class="p">()</span>
<span class="linenos">129</span><span class="n">data</span> <span class="o">=</span> <span class="n">compute</span><span class="p">(</span><span class="n">clusters</span><span class="p">)</span>
<span class="linenos">130</span><span class="n">data</span> <span class="o">=</span> <span class="n">analysis</span><span class="p">(</span><span class="n">data</span><span class="p">)</span>
<span class="linenos">131</span><span class="n">data</span><span class="o">.</span><span class="n">view</span><span class="p">()</span>
<span class="linenos">132</span>
</pre></div>
</div>
</div>

41
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@ -57,10 +57,12 @@
<script async="async" src="../_static/sphinx-thebe.js?v=c100c467"></script>
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@ -189,7 +191,7 @@
<li class="toctree-l1"><a class="reference internal" href="../Activity07/Activity07.html">Activity 7: Large clusters and path filtering</a></li>
<li class="toctree-l1"><a class="reference internal" href="../Activity08/Activity08.html">Activity 8: Inequivalent emitters and the XPD of a substrate</a></li>
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<li class="toctree-l1"><a class="reference internal" href="../backmatter.html">Final word</a></li>
</ul>
@ -317,7 +319,9 @@ document.write(`
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</script>
<button class="sidebar-toggle secondary-toggle btn btn-sm" title="Toggle secondary sidebar" data-bs-placement="bottom" data-bs-toggle="tooltip">
<span class="fa-solid fa-list"></span>
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@ -333,6 +337,14 @@ document.write(`
<div id="print-main-content">
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<h2> Contents </h2>
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<nav aria-label="Page">
<ul class="visible nav section-nav flex-column">
<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#the-unusual-tilt-of-co-molecule-on-fe-001">The unusual tilt of CO molecule on Fe(001)</a></li>
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@ -344,6 +356,12 @@ document.write(`
<section class="tex2jax_ignore mathjax_ignore" id="activity-9-comparing-simulation-and-experiment-with-r-factors">
<h1>Activity 9: Comparing simulation and experiment with R-factors<a class="headerlink" href="#activity-9-comparing-simulation-and-experiment-with-r-factors" title="Link to this heading">#</a></h1>
<p>In order to extract precise crystallographic information from electronic spectroscopy, we need to compare MsSpec calculations with experimental results and adjust the modelling parameters to simulate the experiment as accurately as possible.</p>
<p><em>R-factors</em> (reliability factors) are commonly used for this task. In the following example, we will see how MsSpec can extract the adsorption geometry of molecule.</p>
<section id="the-unusual-tilt-of-co-molecule-on-fe-001">
<h2>The unusual tilt of CO molecule on Fe(001)<a class="headerlink" href="#the-unusual-tilt-of-co-molecule-on-fe-001" title="Link to this heading">#</a></h2>
<p>The carbon monoxide molecule can be adsorbed onto a Fe(001) surface in the hollow site. It was experimentally demonstrated that the CO molecule is tilted by 55<span class="math notranslate nohighlight">\(\pm\)</span>2° in &lt;100&gt; azimuthal directions. The molecule is bonded to the Fe surface by the carbon atom and the adsorption height was estimated to be <span class="math notranslate nohighlight">\(\sim\)</span> 0.6 Å.</p>
</section>
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<div class="bd-sidebar-secondary bd-toc"><div class="sidebar-secondary-items sidebar-secondary__inner">
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@ -8,7 +8,7 @@
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<title>Activity 10: Auger Electron Diffraction &#8212; MsSpec Tour</title>
<title>Activity 10: Parallelization and multi-processing in MsSpec &#8212; MsSpec Tour</title>
@ -189,7 +189,7 @@
<li class="toctree-l1"><a class="reference internal" href="../Activity07/Activity07.html">Activity 7: Large clusters and path filtering</a></li>
<li class="toctree-l1"><a class="reference internal" href="../Activity08/Activity08.html">Activity 8: Inequivalent emitters and the XPD of a substrate</a></li>
<li class="toctree-l1"><a class="reference internal" href="../Activity09/Activity09.html">Activity 9: Comparing simulation and experiment with R-factors</a></li>
<li class="toctree-l1 current active"><a class="current reference internal" href="#">Activity 10: Auger Electron Diffraction</a></li>
<li class="toctree-l1 current active"><a class="current reference internal" href="#">Activity 10: Parallelization and multi-processing in MsSpec</a></li>
<li class="toctree-l1"><a class="reference internal" href="../Activity11/Activity11.html">Activity 11: Spectral radius and convergence</a></li>
<li class="toctree-l1"><a class="reference internal" href="../backmatter.html">Final word</a></li>
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@ -328,7 +328,7 @@ document.write(`
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<h1>Activity 10: Auger Electron Diffraction</h1>
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@ -342,8 +342,8 @@ document.write(`
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<h1>Activity 10: Parallelization and multi-processing in MsSpec<a class="headerlink" href="#activity-10-parallelization-and-multi-processing-in-msspec" title="Link to this heading">#</a></h1>
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6
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@ -61,7 +61,7 @@
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
<link rel="next" title="Final word" href="../backmatter.html" />
<link rel="prev" title="Activity 10: Auger Electron Diffraction" href="../Activity10/Activity10.html" />
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@ -189,7 +189,7 @@
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<li class="toctree-l1"><a class="reference internal" href="../Activity08/Activity08.html">Activity 8: Inequivalent emitters and the XPD of a substrate</a></li>
<li class="toctree-l1"><a class="reference internal" href="../Activity09/Activity09.html">Activity 9: Comparing simulation and experiment with R-factors</a></li>
<li class="toctree-l1"><a class="reference internal" href="../Activity10/Activity10.html">Activity 10: Auger Electron Diffraction</a></li>
<li class="toctree-l1"><a class="reference internal" href="../Activity10/Activity10.html">Activity 10: Parallelization and multi-processing in MsSpec</a></li>
<li class="toctree-l1 current active"><a class="current reference internal" href="#">Activity 11: Spectral radius and convergence</a></li>
<li class="toctree-l1"><a class="reference internal" href="../backmatter.html">Final word</a></li>
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@ -382,7 +382,7 @@ document.write(`
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4
msspecbook/_build/html/_downloads/0e4320262cbcdc4d473d0b9d43e0f7e9/AlN.py
View File

@ -1,7 +1,3 @@
#!/usr/bin/env python
# coding: utf8
from ase.build import bulk
import numpy as np
from msspec.calculator import MSSPEC, XRaySource

2
msspecbook/_build/html/_sources/Activity07/Activity07.ipynb
View File

@ -187,7 +187,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.11.13"
"version": "3.11.3"
}
},
"nbformat": 4,

4
msspecbook/_build/html/_sources/Activity08/Activity08.ipynb
View File

@ -143,7 +143,7 @@
"\n",
":::{literalinclude} AlN_completed.py\n",
":lineno-match:\n",
":emphasize-lines: 1\n",
":emphasize-lines: 8,31-34,60,61,63,64,66,68,69,71\n",
":::\n",
"\n",
"```"
@ -166,7 +166,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.11.13"
"version": "3.11.3"
}
},
"nbformat": 4,

17
msspecbook/_build/html/_sources/Activity09/Activity09.ipynb
View File

@ -1,20 +1,19 @@
{
"cells": [
{
"attachments": {},
"cell_type": "markdown",
"id": "aa43e0e7-0c18-4750-9e2b-3a48f106d2ca",
"metadata": {},
"source": [
"# Activity 9: Comparing simulation and experiment with R-factors"
"# Activity 9: Comparing simulation and experiment with R-factors\n",
"In order to extract precise crystallographic information from electronic spectroscopy, we need to compare MsSpec calculations with experimental results and adjust the modelling parameters to simulate the experiment as accurately as possible.\n",
"\n",
"*R-factors* (reliability factors) are commonly used for this task. In the following example, we will see how MsSpec can extract the adsorption geometry of molecule.\n",
"\n",
"## The unusual tilt of CO molecule on Fe(001)\n",
"The carbon monoxide molecule can be adsorbed onto a Fe(001) surface in the hollow site. It was experimentally demonstrated that the CO molecule is tilted by 55$\\pm$2° in <100> azimuthal directions. The molecule is bonded to the Fe surface by the carbon atom and the adsorption height was estimated to be $\\sim$ 0.6 Å."
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "b9b32bbf-7635-4e14-b246-468f2e74bb17",
"metadata": {},
"outputs": [],
"source": []
}
],
"metadata": {

4
msspecbook/_build/html/_sources/Activity10/Activity10.ipynb
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@ -5,7 +5,7 @@
"id": "38d3e621-e866-43e1-9c92-f473d1e755c0",
"metadata": {},
"source": [
"# Activity 10: Auger Electron Diffraction"
"# Activity 10: Parallelization and multi-processing in MsSpec"
]
},
{
@ -33,7 +33,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.11.3"
"version": "3.11.13"
}
},
"nbformat": 4,

2
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@ -188,7 +188,7 @@
<li class="toctree-l1"><a class="reference internal" href="Activity07/Activity07.html">Activity 7: Large clusters and path filtering</a></li>
<li class="toctree-l1"><a class="reference internal" href="Activity08/Activity08.html">Activity 8: Inequivalent emitters and the XPD of a substrate</a></li>
<li class="toctree-l1"><a class="reference internal" href="Activity09/Activity09.html">Activity 9: Comparing simulation and experiment with R-factors</a></li>
<li class="toctree-l1"><a class="reference internal" href="Activity10/Activity10.html">Activity 10: Auger Electron Diffraction</a></li>
<li class="toctree-l1"><a class="reference internal" href="Activity10/Activity10.html">Activity 10: Parallelization and multi-processing in MsSpec</a></li>
<li class="toctree-l1"><a class="reference internal" href="Activity11/Activity11.html">Activity 11: Spectral radius and convergence</a></li>
<li class="toctree-l1 current active"><a class="current reference internal" href="#">Final word</a></li>
</ul>

2
msspecbook/_build/html/genindex.html
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@ -188,7 +188,7 @@
<li class="toctree-l1"><a class="reference internal" href="Activity07/Activity07.html">Activity 7: Large clusters and path filtering</a></li>
<li class="toctree-l1"><a class="reference internal" href="Activity08/Activity08.html">Activity 8: Inequivalent emitters and the XPD of a substrate</a></li>
<li class="toctree-l1"><a class="reference internal" href="Activity09/Activity09.html">Activity 9: Comparing simulation and experiment with R-factors</a></li>
<li class="toctree-l1"><a class="reference internal" href="Activity10/Activity10.html">Activity 10: Auger Electron Diffraction</a></li>
<li class="toctree-l1"><a class="reference internal" href="Activity10/Activity10.html">Activity 10: Parallelization and multi-processing in MsSpec</a></li>
<li class="toctree-l1"><a class="reference internal" href="Activity11/Activity11.html">Activity 11: Spectral radius and convergence</a></li>
<li class="toctree-l1"><a class="reference internal" href="backmatter.html">Final word</a></li>
</ul>

4
msspecbook/_build/html/intro.html
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@ -192,7 +192,7 @@
<li class="toctree-l1"><a class="reference internal" href="Activity07/Activity07.html">Activity 7: Large clusters and path filtering</a></li>
<li class="toctree-l1"><a class="reference internal" href="Activity08/Activity08.html">Activity 8: Inequivalent emitters and the XPD of a substrate</a></li>
<li class="toctree-l1"><a class="reference internal" href="Activity09/Activity09.html">Activity 9: Comparing simulation and experiment with R-factors</a></li>
<li class="toctree-l1"><a class="reference internal" href="Activity10/Activity10.html">Activity 10: Auger Electron Diffraction</a></li>
<li class="toctree-l1"><a class="reference internal" href="Activity10/Activity10.html">Activity 10: Parallelization and multi-processing in MsSpec</a></li>
<li class="toctree-l1"><a class="reference internal" href="Activity11/Activity11.html">Activity 11: Spectral radius and convergence</a></li>
<li class="toctree-l1"><a class="reference internal" href="backmatter.html">Final word</a></li>
</ul>
@ -362,7 +362,7 @@ concepts needed to learn how to perform simulation with MsSpec.</p>
<li class="toctree-l1"><a class="reference internal" href="Activity07/Activity07.html">Activity 7: Large clusters and path filtering</a></li>
<li class="toctree-l1"><a class="reference internal" href="Activity08/Activity08.html">Activity 8: Inequivalent emitters and the XPD of a substrate</a></li>
<li class="toctree-l1"><a class="reference internal" href="Activity09/Activity09.html">Activity 9: Comparing simulation and experiment with R-factors</a></li>
<li class="toctree-l1"><a class="reference internal" href="Activity10/Activity10.html">Activity 10: Auger Electron Diffraction</a></li>
<li class="toctree-l1"><a class="reference internal" href="Activity10/Activity10.html">Activity 10: Parallelization and multi-processing in MsSpec</a></li>
<li class="toctree-l1"><a class="reference internal" href="Activity11/Activity11.html">Activity 11: Spectral radius and convergence</a></li>
<li class="toctree-l1"><a class="reference internal" href="backmatter.html">Final word</a></li>
</ul>

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msspecbook/_build/html/search.html
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@ -190,7 +190,7 @@
<li class="toctree-l1"><a class="reference internal" href="Activity07/Activity07.html">Activity 7: Large clusters and path filtering</a></li>
<li class="toctree-l1"><a class="reference internal" href="Activity08/Activity08.html">Activity 8: Inequivalent emitters and the XPD of a substrate</a></li>
<li class="toctree-l1"><a class="reference internal" href="Activity09/Activity09.html">Activity 9: Comparing simulation and experiment with R-factors</a></li>
<li class="toctree-l1"><a class="reference internal" href="Activity10/Activity10.html">Activity 10: Auger Electron Diffraction</a></li>
<li class="toctree-l1"><a class="reference internal" href="Activity10/Activity10.html">Activity 10: Parallelization and multi-processing in MsSpec</a></li>
<li class="toctree-l1"><a class="reference internal" href="Activity11/Activity11.html">Activity 11: Spectral radius and convergence</a></li>
<li class="toctree-l1"><a class="reference internal" href="backmatter.html">Final word</a></li>
</ul>

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